Ilos:
Shepard eventually woke up still wrapped in Kaidan's arms. Kaidan was still fast asleep and the two of them were still naked. Shepard smiled and carefully removed Kaidan's arms from around her and she quickly got up and got dressed. When Kaidan woke up, he was smiling "It's been a long time since I met a woman who helped me overcome my past." Kaidan stated
"That was the best night's sleep I've had in a long time." Shepard smiled "After everything that's happened, I needed that."
"I think we both did." Kaidan stated "So, where do we go from here?"
"Well assuming we stop Saren, we still have the First Order to deal with." Shepard stated "But also, I need to have a talk with my mother."
"Oh, about what?" Kaidan questioned
"About my life." Shepard admitted "The leader of the First Order wanted me alive and the vision I had on Pandora showed that my mother knows something. I need to know the truth and that's what worries me. What if it something that I don't like? What if it ruins everything I've know?"
Kaidan quickly got out of bed and kissed Shepard deeply on her lips "Whatever the truth is, I will be here for you. Always?"
Shepard smiled and they kissed again until Joker came over the comm "Bridge to Commander Shepard, we're about five minutes from the Mu Relay."
Kaidan laughed "Well, Joker always has a way of ruining the moment." He laughed "You better get to the bridge, you'll need to plan when we get to Ilos. Just make sure that you survive."
"We'll get through this Kaidan." Shepard stated "Together." The two of them kissed once again and then Shepard left to head to the bridge to help plot a course to Ilos.
...
Shepard soon arrived on the bridge where Luke, Bau and Joker were waiting for him. "Do you know what you're doing?" Bau asked Joker
"Aye." Joker replied "I did learn how to use these relays. I just need Shepard to put in the coordinates for Ilos so we can get there. The problem is that the system is not mapped so we don't know what else is there. Travelling via the relay is the only way to find a secure route."
Bau looked at Shepard "What does he mean?"
"Well the Republic uses Hyperdrives to travel but they're not so simple." Shepard replied "If you don't use a good route, you could crash into another planet, fly too close to a black hole or a supernova. There are many different ways that travelling into the unknown can do which is why the Republic used to use the Relays to map routes before we dissembled them. That was what was going on at Shanxi when the Turians found us. I know where we're going, the vision gave me the location of the system where Ilos is and which planet it is in the system." She quickly placed the codes into the Navicomputer and then as the Normandy approached the Mu Relay, the ship was sent towards the location of Ilos.
...
The Normandy soon arrived at its destination. This system was unexplored and so they had no idea what to expect although the vision had shown that the system had been a binary star system meaning it had two moons. As soon as the Normandy arrived, they found that there were three planets in the system and scanners could detect the remains of Prothean ruins on all three planets, one of which was a gas giant and may had been used for mining Helium-3.
The crew could see which one was Ilos as it seemed that the First Order had sent a few Star Destroyers to the system but they could only see three meaning this was a small force and the massive 7 kilometre Dreadnought was nowhere to be seen. The star destroyers were above the second planet in the system so that had to be Ilos. Joker engaged the Stealth Systems and carefully began to approach the planet.
"Have they spotted up?" Bau asked
"The Stealth Systems are engaged." Luke replied "They can't see us unless we fly to close but we may have to do that to send you guys in the Mako."
Navigator Pressley then ran onto the bridge "Commander, we're picking up strange readings from the surface."
"Take us down Joker." Shepard ordered "Lock in on the coordinates."
"I wouldn't recommend that Commander." Pressley stated "The nearest landing site is two clicks away from the location of those ruins." Shepard had been given the location of the conduit from the beacon and she wanted to get as close to them as she can.
"We'll never make it to the Conduit from that distance in time." Kaidan shouted "Give us something closer."
"There is nowhere closer!" Pressley snapped "I've looked."
"Then I guess we'll have to take our chances in the Mako." Shepard stated
"Shepard, you need at least a hundred feet of open terrain to land safely." Pressley stated "The most I can find near the location where you want to land is twenty."
"Twenty meters!" Kaidan snapped "No way we can make a drop like that."
"We have to try." Pekue added "I can do it."
"Our decent is too steep." Tali added
"We have no choice." Liara shouted "If we land to far then we'll miss our chance to catch Saren."
"This is not an option!" Kaidan shouted "It's a suicide run! We don't..."
"I can do it." Pekue stated "But we'll have to be very close to get a good drop."
"That means we're probably going to be spotted." Luke stated
"I know what to do." Joker added and then looked at Shepard "Get you team into the Mako, when I tell you to drop, drop the shuttle. But I'm afraid you will be on your own as I'll have to leave here before we get destroyed." He then turned forward and muttered "If we don't break up in the atmosphere that it."
"Alright." Shepard stated "I hope this works."
...
Down on Ilos, Saren had just managed to get the doors open to head inside the ruined Prothean complex. After the fight on Virmire, he had a new replacement arm to replace the one that he had lost and now he was ready to make his move. All he needed was to find the Conduit and it would begin. He held out a hologram transmitted and made a call but it was not to his master. Instead it was to a middle aged man with greying hair "Captain Canady, are you forces in position."
"We are Sir." The man known as Canady replied in a cold stern voice "Our forces are ready when you give the order."
"Good." Saren stated "Once we've found the conduit, head straight to the City and fire on the Citadel fleet. Don't wait for any kind of call, just attack."
"Understood." Canady replied and Saren ended the call.
"My lord." One of his troopers called "Our ships just spotted a ship matching the description of the RSV Normandy heading to our location."
Saren looked up and could see the Normandy slowly heading downwards avoiding fire from the Star Destroyers. He groaned and looked at some of his troops "You lot, hold them off as long as you can. I won't let them ruin our plan!" the troops nodded and then he went inside locking the door as he did.
...
Shepard and all of her teammates soon got into the Mako and waited for Joker to give the signal. The Normandy shot past the Star Destroyers and headed towards the surface. There were a few tense moments as the Normandy started burning as they travelled through the atmosphere. If something went wrong then they could burn up or break apart. Then the Normandy levelled out "GO NOW!" Joker shouted and Pekue drove the Mako from the Hanger and dropped to the surface and the Normandy lifted up and quickly left Ilos and flee the Star Destroyers who had spotted them.
"Brace!" Pekue shouted and everyone braced in their seats as the Mako landed roughly and Pekue slammed the brakes on and stopped just before the Mako crashed right into the Blast doors that Saren had just sealed.
The troopers who had been left behind started firing on the Mako and so Shepard got her team ready to fight as they fired back as soon as Pekue opened the Mako's doors. Tali manned the cannon and fired back at the troopers before they could fire rockets at the Mako as they would be vulnerable to them as there was no move to move around to avoid fire. The Mako was a sitting duck. When the area was clear, Shepard gathered everyone at the Mako.
Kaidan took one look at the door before he activated his lightsaber and cut through. He leaned his head against the door before he sighed "It's no good." He stated "There is no way our lightsabers can cut through this door, it's too thick."
"And my explosives will do no good either." Bakira added.
"Then what do we do?" Liara asked
"Well Saren opened the door so there has to be controls." Garrus suggested
"Garrus is right." Shepard stated "Bau, Kaidan, Tali and me will look around for some controls in the lower levels. The rest of you stay here and guard the Mako."
"We have to hurry Shepard." Bau stated "The more time we waste, the closer Saren is to the Conduit."
"Well then, let's hurry." Shepard stated and the team quickly split up with Shepard and her group heading to the lower levels.
...
Amazingly, the controls for the elevators still worked and Shepard's team were able to activate the elevators to reach the lower levels. They treaded carefully as this was the perfect spot for an ambush as their instincts were right. It seemed that Saren had brought most of his remaining Geth including a few large Geth Armatures and made them ready for an ambush. The Armatures had been damaged and were on charging stations which Tali hacked causing them to explode destroy the Geth.
Shepard's team had to fight their way through several rooms full of Geth until they came to what looked like a control room which was just above where they landed as they could see the Mako. Shepard found a control panel and could read the controls probably thanks to the Cipher. She quickly activated the controls and they watched as the door opened.
"That did it." She stated "The door's open."
"Come on, let's head back to the Mako." Bau shouted "Saren's already got a head start on us."
"We have to find him before he reaches the Conduit." Kaidan added
"Unless he's already found it and we're walking into a trap." Tali stated "He most likely knows that we're here."
"We'll have to take that risk. We need to..." Bau stated but then he paused "Wait, what's that?"
Shepard turned and saw some kind of holographic projector trying to broadcast audio but it wasn't clear "Too late." It said before going back to static "unable to... invading fleets... no escape..."
"That sounds like some kind of message but I can't make up a word of it." Tali stated
"Wait, I can." Shepard stated "you guys can't hear, the message is scrambled but I can understand a few bits."
"It's probably in Prothean." Bau gasped "This is an old Prothean outpost. The Cipher seems to allow you to understand it."
"The message must have been damaged at some point." Shepard replied "It seems to be a warning."
The recording began again. "Not safe... seek refuge... beside the archives... The Citadel... overwhelmed... only hope..." the voice then changed slightly "Act of desperation... the Conduit... all is lost... beware... the Star Forge... darkness... turned."
"What's it saying; can you make out anything useful that could help us find the Conduit?" Bau asked
Shepard shook her head "It just said something about the Conduit, but it's too degraded to help. There was also something else about something called the Star forge but I have no idea what that is. We should go, we can't waste time."
They left the room to start heading back to the Mako as they heard the consol say "Cannot be stopped."
...
Shepard's team made it back to the Mako and with the door now unlocked, Pekue began driving through the long tunnel carefully as they were expecting an ambush so they manned the guns ready for a fight. But to their surprise, there was nothing.
"I thought Saren would have launched an ambush." Bau stated as they drove through.
"Maybe we've just not got to it yet." Kaidan stated
Garrus looked out of the Mako's window and saw that the walls of the long tunnel were line with glass tubes "What's with all of these?" he questioned
Liara joined him "They look like stasis pods" she stated "The Protheans must have used cryo freezing to freeze themselves as a last ditch effort to survive. Something must have gone wrong, this safe place became their tomb."
"What could have gone wrong?" Kaidan asked
"Lots of different things." Liara stated "There could have been a power loss, they could have been damaged. Cryo freezing is much more dangerous than you think. The one you found on Eden Prime is an exception."
Shepard had honestly nearly forgotten about the Prothean Stasis Pod they had found on Eden Prime along with the beacon. After dealing with Saren, she would need to check up on that. Then the Mako stopped "Pekue, what's happening?"
"Shepard, our path is blocked." Pekue called "He's created some sort of barrier, there's no way we can get through this?"
"So what do we do now?" Bau asked
"Well maybe you can shut it down?" Pekue suggested "There's a small corridor here, maybe it leads to the control room."
"Alright" Shepard stated and stood up "Bau, Kaidan, Tali and Liara. You're with me. The rest of you, stay behind and keep an eye out for any Geth that we may have past." They nodded and Shepard's team quickly left the Mako and went down the small corridor. They came into a small elevator which then took them down to a small room. To their surprise, they saw a ghostly white figure standing before them.
The figure looked like an alien but not like any they had ever seen before. It had a scaly body and had two pairs of eyes like a Batarian but each had two pupils. It also had three sets of nostrils and had a head covered in a thick layered carapace. It also wore a long brown cloak "You are not Prothean, but you are also not machine or have the darkness. This was one of many scenarios that was anticipated."
"What is this?" Liara asked
"At first I would have believed it to some kind of a Prothean VI but it doesn't seem to be." Bau stated
The figure laughed "No, I am not a VI. You could say I am a spirit, a ghost. I am one with the force."
"One with the Force" Kaidan gasped "I remember reading about this in the Temple, Jedi who were well trained in the force could still live as force ghosts and give advice to other Jedi when they needed it."
"You are correct." The figure added "My name is Vigil, the spirit of a Prothean who lived and died here in one of the last Great Battles of my people."
"You're a Prothean?" Liara gasped "Your people have not been seen in 50,000 years."
"Yes, my people have died out by now. Our attempt of surviving failed and the cycle will begin again but maybe you can stop it. I may be dead but I can still give you a warning which was why I brought you here." Vigil replied
Tali then noticed something "Wait, how come we can understand you, the other console was all in Prothean."
"I may have passed but I still have the Prothean ways of analysing you." Vigil stated "I have reached into your minds and have gained an understanding of your language. You are safe here but that is likely to change. Soon nowhere will be safe, you have to prevent a repeat of the past."
"What are you talking about?" Shepard asked
"You have to break a cycle that had continued for millions of years." Vigil stated "But to stop it, you must understand or you will repeat our mistakes. You surely know of the Citadel, the seat of our government and galactic Power, but this is a trap. The station is actually a giant mass Relay, one that connects with Dark Space, the empty void between galaxies. When the Citadel Relay is activated, the Reapers will pour through and destroy all that you know."
Bau gasped "That means that the Council could be wiped out. While the Republic will be safe, the Council members will fight to protect their own."
"When the Reapers first appeared, the centre of our government was destroyed before we even had a chance to know what was going on." Vigil replied "The Reapers seized control of the Citadel Relay and could then jump to pretty much anywhere in the galaxy. Communication and transportation across our Empire was crippled, we were isolated and easy prey. World by world, system by system, my people were wiped out over the decades. We tried to fight back but had no luck. The Reapers were killing our soldiers faster than we could recruit. Our navy was getting destroyed faster than we could replace our ships."
"So the Reapers wiped out your people?" Liara stated
"That is not the end of the story." Vigil stated "The war did not happen quickly, my people were still able to put up a fierce resistance. We did not go down without a fight. We eventually turned to a new way of fighting. We looked to the ways of the Rakata."
"The Rakata?" Liara questioned
"An Ancient race of aliens that were around at the same time my people were." Vigil stated "The Rakata at one point were the dominant species in the galaxy. They had a massive Empire compared to us as we were still just a rising power. Eventually, our Empires classed, the war lasted years but eventually, my people succeeded. The Rakatan's Infinity Empire collapsed and we began taking over as the new masters of the galaxy, The Rakatan's would eventually go extinct after they collapsed into infighting. But they had a unique way of fighting, the ways of the force."
"The Force, like the Jedi?" Kaidan questioned
"I do not know of the word Jedi" Vigil stated "But we began teacher ourselves to use the force and we gained new abilities which allowed us to fight the Reapers better as they had no way of fighting this new power. While we were fighting, one of our leaders heard of an ancient weapon of the Rakatan known as the Star Forge."
"The Star Forge?" Shepard gasped "I heard a mention about that on the recording but it was too degraded to understand."
"The Star Forge was a ancient Space weapon that was capably of building entire fleets of ships." Vigil stated "It drew on the power of the stars to create fleets and when we recovered it, we were able to replace our losses much quicker and as the Reapers were unaware of the Star Forge, it was safe. We soon came close to defeating the Reapers."
"But if you came close then what happened?" Liara asked "Did something else happen?"
"It did." Vigil stated "We were unaware of it but the Star Forge was a source of evil. The Rakatan were a cruel species who brutally subjugated many different species and used slaves to construct the station. The station became alive in a way that it began to affect our Leadership. Our own people began to start fighting each other. Our Great leader who had once discovered the Star Forge turned against us and became a tyrant. We all started fighting each other and we soon lost control of the Star Forge which was now used against us. The Star Forge became a weapon for this group who came to be known as the Sith."
"The Sith?" Kaidan gasped "This was where the order of the Sith came from."
"They claimed they would bring order to the galaxy. They had strong support as the leaders had been victorious in dealing with the Reapers but they wanted to rule the galaxy. We started fighting each other and soon, the Reapers gained the upper hand in the war again. They cut off access to the Star Forge and since we were constantly fighting each other now, we couldn't hold them off and soon, my people were driven to the brink of extinction again."
"But just what are the Reapers?" Bau asked
"The Reapers were a name that we gave to these machines." Vigil replied "We believed that they had been some kind of AI gone wrong. They may have been some kind of population control that turned against their creators and so, they destroy the galaxy's population each cycle and allow new species to take over. At least, that what we think, it's hard to understand what the Reaper's intentions."
"So what happened in the end?" Liara asked
"With the Reapers all but about to win, it was decided that we would have to go into hiding." Vigil stated "Ilos was a top secret research base, so secret that very few knew about it. This place was meant to be for researching the secrets of using Mass Relay technology. But before the end, we discovered a way that could at least give the next cycle a chance, the Conduit."
"The Conduit?" Bau gasped "That's what Saren's looking for."
"The Conduit is not a weapon, it's a passageway." Vigil stated "A mini Mass Relay that takes you straight to the Citadel."
"You mean the Conduit is a backdoor to the Citadel?" Tali gasped
"So Saren's going to head back to the Citadel, but why?" Bau realized
"The one who was here before was full of darkness." Vigil stated referring to Saren "If he is working for the Reapers then he might be trying to undo what we did. You see, we sent a team through the Conduit to shut down the signal that would inform the Reapers when it was time to return. When the harvesting is ready to begin, the Keepers would send the Reapers the transmission codes to use the Citadel Relay."
"The Keepers, you mean the little maintenance people?" Bau questioned
"The Keepers may have been the first species harvested by the Reapers and used as their slaves." Vigil stated
"But what about the Reaper Sovereign?" Shepard questioned "How did he get here? Also, Saren's working for the First Order who wants to control the Reapers?"
"The Reapers may have left one of their own behind each cycle as a way of watching when the time is right to harvest." Vigil suggested "As for what you've just said, the Sith back in my cycle had the same idea about trying to control the Reapers. They wanted to use them as a way of taking control of the galaxy."
"I guess that means we may fall into the same trap the Protheans did if we don't stop the First Order." Bau stated
"But what happened here at Ilos?" Liara asked
"After we sent the team through the Conduit, they never came back as it's a one way trip." Vigil stated "And afterwards, all of the Protheans sealed themselves away in cryo pods which you saw when you travelled down the tunnel. Our hope was to remain hidden until the danger had past. But we never could see what would happen. It turned out that we were not the only Prothean survivors. Other groups had managed to survive but these were ones who took up the Sith Code. They saw us as a threat and so they bomb us, destroying the life support of the Cryo pods and dooming those inside, myself included but I was able to use my teachings to remain here in spirit form. I am bound to this place which meant I could control parts of the base which is why I brought you here to give you my warning personally."
"So what can I do?" Shepard asked
"You have a chance to stop the Reapers from returning." Vigil stated "This Saren can use the Conduit to bypass Citadel security and give control of the Citadel to Sovereign. Then Sovereign can activate the Relay and allow the Reapers to return."
"Saren must have something else to allow the First Order to control the Reapers then." Bau stated
"It is possible." Vigil stated "If the Sith have indeed remained all these years then maybe they've found a way to control the Reapers. If you wish to stop the Reapers from returning then you will need a copy of a data file in the console in this room. When you reach the Citadel's Master Control centre at the top of the tower in the middle ring of the Citadel, upload it to the station, it will corrupt the security protocols and give you control of the Citadel."
"That means the Master Control Centre is at the Council chambers." Bau stated
"Then we need to get going now." Shepard stated "Saren could be near the Conduit by now and he has a head start on us. We need to get to him fast. Tali, download that file and let's get back to the Mako." Everyone nodded and Tali quickly downloaded the file from the console and they quickly headed back up the elevator to the Mako.
"Good luck to all of you. And may the force be with you." Vigil called as they left the room.
...
Meanwhile, Saren had arrived at the Conduit which was a mini Mass Relay. He had a large group of his forces in armoured vehicles to take them through the Relay and strike the Citadel from within. First Order forces led by Captain Canady would strike at the Citadel fleet as a distraction. Saren was now in contact with Canady again "Captain, it is time." He ordered "Begin the attack."
"Yes sir!" Canady ordered
Saren ended the call and looked at one of his commanders "Stay here and hold off that Republic squadron."
"As you command." The man said.
Saren then looked at his driver "All right everyone, drive through the Conduit."
The armoured vehicle quickly drove through the Conduit and was followed by numerous other vehicles and Saren smirked, soon his mission would be complete and there was nothing that could stop him.
Chapter End:
Notes: Well, I decided to end the chapter here. I plan to write the Battle of the Citadel in more detail showing the actual fighting. So there might be two chapters for that section. Not far off finishing this story now and I should have this story finished by the end of August, maybe earlier but the next chapter may be difficult to write as much of it will be of a battle. We'll just have to wait and see how things go. I also brought in the Star Forge and the Rakatan people from the Knights of the Old Republic. When I finished playing that game, I knew I had to bring them in and so I made the Rakatan as an species that had fought against the Protheans while they were rising to power and ultimately lost and then the Rakatan were wiped out in a Civil War. Now I know the Rakatan in Star Wars were seen as a species who had created a way of hyperspace travel but in this, they did not but were seen by the Protheans as the creators of the Mass Relays but they really weren't. The Star Forge will play a role in the future as well. The Mass Effect 2 story will have more differences from the original than this story as I plan to explain more of the Jedi-Sith conflict in that one as well as explore more of the past. In fact, I plan on giving Liara a bigger role as I have an idea that she will actually go and try to seek the original Prothean homeworld, this would mean having to create a planet as the Protheans have no named planet as their homeworld. If I'm wrong, tell me.